Glossary · Bioinformatics
Alpha and beta diversity
In one sentence
Alpha diversity measures the variety of microorganisms within a single sample (how many types and how evenly spread); beta diversity measures how different two or more samples are from each other.
Also known as: alpha diversity · beta diversity · α-diversity · β-diversity · microbial diversity
What is alpha and beta diversity?
Both terms come from ecology and are now used to describe the microbiota. The ecologist Robert Whittaker formalised them in 1960 in Ecological Monographs, in his study of vegetation in the Siskiyou Mountains: alpha diversity is the diversity of a particular site, and beta diversity is the extent of change in composition between sites.
In the laboratory, each sample (stool, saliva, a vaginal swab) is a “site”. Alpha diversity answers “how much variety is there here?” and beta diversity answers “how similar is this sample to others?”.
How it is measured
Alpha diversity combines two ideas: richness (how many distinct taxa are present) and evenness (whether they are evenly spread or a few dominate). Common indices include:
- Observed richness: the number of taxa detected.
- Shannon index: accounts for both richness and evenness.
- Simpson index: gives more weight to dominant taxa.
- Chao1: estimates total richness, correcting for rare taxa that were missed.
Beta diversity is calculated as a distance or dissimilarity between pairs of samples. The most widely used are Bray-Curtis (based on relative abundance), Jaccard (presence or absence) and UniFrac (which adds phylogenetic relatedness). Results are usually plotted in ordination charts such as PCoA, where similar samples sit close together.
How to interpret it
- Values depend on method: sequencing depth, technique (16S or metagenomics), the use of OTUs or ASVs and the reference database. Figures are not comparable between laboratories unless the same pipeline is used.
- Observational studies have linked low gut diversity with dysbiosis, recent antibiotic use and inflammatory bowel disease, but association is not causation.
- What counts as “normal” depends on the site: low diversity dominated by Lactobacillus is typical of a healthy vagina.
Example
A gastroenterologist reviews a stool microbiota report for a patient who finished a course of antibiotics two months earlier. Alpha diversity sits below the laboratory’s reference interval, and the beta diversity plot places the sample away from the healthy comparison group. The doctor records this as context alongside the symptoms and considers repeating the test later to follow the trend, rather than treating it as a diagnosis.
Alpha and beta diversity at Xenogene
According to its product page, the Gut Microbiota test includes bacterial diversity as part of a full metagenomic stool analysis. In the Essential Microbiota test, the report presents alpha diversity (richness and evenness) and beta diversity as a comparison with a healthy population. Interpretation is the responsibility of the requesting clinician, together with the clinical history.
Frequently asked questions
What does low gut microbiome diversity mean?
It means the sample contains fewer types of microorganism, or that a few of them dominate. Many studies associate low diversity with dysbiosis and some diseases, but this is an association: on its own it is not a diagnosis and needs to be read in clinical context.
What is the difference between alpha and beta diversity?
Alpha diversity describes one sample: its richness and evenness. Beta diversity compares samples, for example a patient against a reference population, or the same person before and after treatment.
Is higher diversity always better?
Not always. In the adult gut it is generally regarded as favourable, but in other sites, such as a healthy Lactobacillus-dominated vaginal microbiota, low diversity is what you would expect.
Related terms
- Shannon index
The Shannon index is an alpha diversity measure that combines how many types of microorganism are present in a sample and how evenly they are distributed: the higher the value, the more diverse the community.
- Relative abundance
Relative abundance is the share of a microorganism in the total detected in a sample, usually given as a percentage. It reflects its weight within the community, not its absolute quantity.
- OTU and ASV
OTUs (operational taxonomic units) group similar DNA sequences, usually at 97% identity; ASVs (amplicon sequence variants) are exact sequences that can be told apart by a single nucleotide.
- Dysbiosis
Dysbiosis is a change in the composition or function of the microbiota away from what is considered compatible with health: loss of diversity, loss of beneficial microbes or overgrowth of others.
- Microbiota
The microbiota is the community of living microorganisms (bacteria, archaea, fungi, protozoa) that inhabits a specific site of the body, such as the gut, mouth, skin or vagina.
Educational content for healthcare professionals and the general public. It does not replace assessment by a healthcare professional: ordering and interpreting any test is the responsibility of the requesting clinician.
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